this page is a work in progress

High-throughput Screening

Cell-based screen of the Mammalian Gene Collection (MGC) for enhancers of STAT1 signaling in Toxoplasma infected cells


Influence of the orphan nuclear receptor TLX on IFN-gamma-dependent gene expression

  • Influence of ectopic TLX expression on transcriptional response of human U20S cells to IFN-gamma (paper; data)
  • Influence of TLX knockdown on the ability of U251 astroglioma cells to respond to IFN-gamma (paper; data).
  • Impact of ectopic TLX expression on mouse myeloid (CD11b+) cells](unpublished; data).

The host response to Leishmania infection

  • Transcriptional profiling of skin from C57BL6 (resistant) or Balb/c (suseptible) mice infected with either Leishmania major or Leishmania braziliensis (unpublished; shiny)

  • Transcriptional profiling of skin biopsies from patients with early or late cutaneous lesions caused by Leishmania braziliensis (paper; data).

  • Early response of immune mouse skin following challenge with Leishmania (paper; data).

  • peripheral blood signatures in patients with Leishmania braziliensis (coming soon!)

Skeletal muscle reprogramming during Trichinella spiralis infection

  • Innate immune-driven transcriptional remodeling of skeletal muscle following infection with the parasitic helminth Trichinella spiralis (paper; data; code).

Host response to Toxoplasma gondii infection

  • Differential induction of type I interferon transcriptional responses by intracellular protozoan parasites (paper; data here and here).

Transcriptional changes in response to defined immune stimuli

  • Kinetics of calcium-induced NFkB-dependent gene expression in Jurkat T cells (paper; data)
  • IFN-gamma-driven, STAT1-dependent gene expression in primary mouse astrocytes (paper; data)
  • Casp8 and Rip3-dependent effects on LPS signaling in mouse macrophages (paper; data; code).

Genome sequences

Genome sequence for Staphylococcus schleiferi

  • see our Genome Announcements paper for more information about the strains used for this study, as well as links to all the associated datasets


Effect of Toxoplasma infection on gut microbiome (shotgun metagenomics)

Investigating an outbreak in Non-SCID Gamma (NSG) mouse colony (shotgun metagenomics)

The microbiome during treatment and remission of diet-responsive inflammatory bowel disease (IBD) in dogs (shotgun metagenomics)

Longitudinal tracking of the gut microbiome in pigs throughout pregnancy (16S V4; shotgun metagenomics)